I really appreciate your help. But what puzzles me is whether you are suggesting me run with NVE or just try it in NVE to insure it is an equilibrium simulation.
If it’s the first case, the task is simulating the nanotube under various temperatures. We may set energy in NVE. But can temparature be set to a fixed value (i.e.2800K)in it?
If it’s the second case, I think my initial structure is stable, otherwise it is impossible to run the simulation under lower temperatures.
(Sorry, I don’t know where to send this email because it’s my first time to use the mailing list. If it makes anyone bored, please forgive me. )
I'm suggesting you run as simple as possible a simulation
(e.g. NVE instead of NVT) to figure out why you are losing
atoms. Presumably some atom(s) is experiencing a large
force and being kicked out of the simulation. You need to
figure out why, by monitoring thermodyamics, dumping frequent
snapshots, etc. Running NVT may mask the effect, or delay it.